As of August 31st, 2023 the Staphopia API has reached end-of-life

If your research was affected by this shut down, please reach out to Tim Read and/or Robert Petit.

staphopia-r

A R library to extract data from the Staphopia API

Installation

Tested on R version 3.4

First install the Bioconductor Biostrings and devtools package (if not already installed)

source("https://bioconductor.org/biocLite.R")
biocLite("Biostrings")
install.packages("devtools")
library(devtools)

Install and test staphopia-r from github (running the test might take 1-2 min)

install_github("staphopia/staphopia-r/staphopia")
library("staphopia")
test_staphopia()

On Mac/ Linux

Create a file in your home directory called ".staphopia" for logging into the API. The file should contain two lines.

TOKEN = "xxxxxxxxxxxxxxxxxxxxxx"
USE_DEV = FALSE

For 'TOKEN' substitute the API authenication token string acquired as described above (USE_DEV is a variable for script development and can be ignored)

On Windows

TBD

Example Commands